Habitual sleep duration varies greatly among individuals. The neurobiological basis of this variation is unknown, but genetic factors play a role as is evident from studies in humans and animals. The timing and duration of sleep are regulated by the interaction of the circadian pacemaker in the suprachiasmatic nucleus of the hypothalamus, and the sleep homeostat. The latter represents an hourglass-like process that keeps track of the increase of sleep pressure during waking and its decrease during sleep. Either one of the two sleep regulatory systems might differ among individuals and affect habitual sleep duration. The present study was designed to gain further insight into the homeostatic system of natural short sleepers (sleep duration <6 hours) and long sleepers (>9 hours). The sleep-wake dependent changes in homeostatic sleep pressure are reflected by quantitative changes in the electroencephalogram. In the present study, we quantified the electroencephalogram during wakefulness and sleep to study the homeostatic sleep regulatory process in natural short sleepers and long sleepers. After sleeping according to their habitual schedule, nine short sleepers (sleep duration <6 h) and eight long sleepers (>9 h) were recorded half-hourly during ~40 h of sustained wakefulness in a constant routine protocol. The electroencephalogram was subjected to spectral analysis. Within the frequency range of 0.25-20.0 Hz, spectral power density in the 5.25-9.0 Hz and 17.25-18.0 Hz ranges was higher in short sleepers than in long sleepers. In both groups, increasing time awake was associated with an increase of theta/low frequency alpha activity (5.25-9.0 Hz), whose kinetics followed a saturating exponential function. The time constant did not differ between groups and was similar to the previously obtained time constant of the wake-dependent increase of slow-wave activity (0.75-4.5 Hz) in the sleep electroencephalogram of healthy volunteers with average sleep duration. In addition, the time constant of the decrease of slow-wave activity during extended recovery sleep following the constant routine did not differ between groups. However, short sleepers showed an abiding enhancement of theta/low frequency alpha activity during wakefulness after recovery sleep that was independent of the homeostatic process. It is concluded that while the kinetics of the homeostatic process do not differ between the two groups, short sleepers live under and tolerate higher homeostatic sleep pressure than long sleepers. The homeostat-independent enhancement of theta/low frequency alpha activity in the waking electroencephalogram in the short sleepers may be genetically determined or be the result of long-term adaptation to chronically short sleep.